Chromosome-level genome assembly of the autotetraploid yellow pitaya provides novel insights into evolution of trait patterning in pitaya species with different ploidy [0.03%]
自四倍体黄皮刺茄染色体水平基因组组装提供新视角理解不同倍性刺茄物种中特性的演化规律
Qamar U Zaman,Ali Raza,Liu Hui et al.
Qamar U Zaman et al.
Background: Yellow pitaya (Selenicereus megalanthus, 2n = 4x = 44) breeding remains severely hindered due to the lack of a reference genome. Results: ...
Effects of chromosome number reduction on mitotic and meiotic stability in fission yeast [0.03%]
染色体数目减少对裂殖酵母有丝分裂和减数分裂稳定性的效应
Yueyue Jiang,Yanze Jian,Lingyun Nie et al.
Yueyue Jiang et al.
Background: Genetic information is stored on multiple chromosomes in eukaryotic organisms and is passed on to offspring through cell division. How chromosome number influences cell division and chromosome segregation is n...
Long-read detection of transposable element mobilization in the soma of hypomethylated Arabidopsis thaliana individuals [0.03%]
长读段检测低甲基化拟南芥个体的体细胞转座元件动员事件
Andrea Movilli,Svitlana Sushko,Fernando A Rabanal et al.
Andrea Movilli et al.
Background: Because transposable elements (TEs) can cause heritable genetic changes, past work on TE mobility in Arabidopsis thaliana has mostly focused on new TE insertions in the germline of hypomethylated plants. It is...
SpaSEG: unsupervised deep learning for multi-task analysis of spatially resolved transcriptomics [0.03%]
SpaSEG：无监督深度学习在空间分辨转录组学多任务分析中的应用
Yong Bai,Xiangyu Guo,Keyin Liu et al.
Yong Bai et al.
Spatially resolved transcriptomics (SRT) for characterizing spatial cellular heterogeneities in tissue environments requires systematic analytical approaches to elucidate gene expression variations within their physiological context. Here, ...
Björn E Langer,Andreia Amaral,Marie-Odile Baudement et al.
Björn E Langer et al.
Standardized analysis pipelines contribute to making data bioinformatics research compliant with the paradigm of Findability, Accessibility, Interoperability, and Reusability (FAIR), and facilitate collaboration. Nextflow and Snakemake, two...
Artificial chromosome reorganization reveals high plasticity of the budding and fission yeast genomes [0.03%]
人工染色体重组揭示出芽和裂殖酵母基因组的高度可塑性
Xueting Zhu,Shaochun Liu,Tiantian Ye et al.
Xueting Zhu et al.
Background: The genome of a eukaryotic cell is usually organized on a set of chromosomes. Recently, karyotype engineering has been applied to various organisms, but whether and to what extent a naturally evolved genome ca...
Field-crop transcriptome models are enhanced by measurements in systematically controlled environments [0.03%]
系统控制环境下的测量可改进田间作物转录组模型
Yoichi Hashida,Daisuke Kyogoku,Suguru E Tanaka et al.
Yoichi Hashida et al.
Background: Plants in the field respond to seasonal and diel changes in various environmental factors such as irradiance and temperature. We previously developed a statistical model that predicts rice gene expression from...
ARTEM: a method for RNA and DNA tertiary motif identification with backbone permutations [0.03%]
一种RNA和DNA三级结构基序识别的算法ARTEM：碱基对排列变化下的结构 motifs 寻找方法
Eugene F Baulin,Davyd R Bohdan,Dawid Kowalski et al.
Eugene F Baulin et al.
Non-coding RNA functions are largely defined by their 3D structures, which consist of recurrent building blocks, tertiary motifs. The computational motif search problem remains largely unsolved, as standard approaches are restrained by sequ...
TRFill: synergistic use of HiFi and Hi-C sequencing enables accurate assembly of tandem repeats for population-level analysis [0.03%]
TRFill：协同使用HiFi和Hi-C测序可准确组装串联重复序列以进行群体水平分析
Huaming Wen,Jinbao Yang,Xianjia Zhao et al.
Huaming Wen et al.
The highly repetitive content of eukaryotic genomes, including long tandem repeats, segmental duplications, and centromeres, makes haplotype-resolved genome assembly hard. Repeat sequences introduce gaps or mis-joins in the assemblies. We i...
David P Hirst,Morgane Térézol,Laura Cantini et al.
David P Hirst et al.
Joint matrix factorization is popular for extracting lower dimensional representations of multi-omics data but loses effectiveness with limited samples. Addressing this limitation, we introduce MOTL (Multi-Omics Transfer Learning), a framew...